IFT43

Summary

IFT43 (intraflagellar transport 43, HGNC:29669) is a protein-coding gene on chromosome 14q24.3, encoding Intraflagellar transport protein 43 homolog (Q96FT9). As a component of IFT complex A (IFT-A), a complex required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), it is involved in ciliogenesis.

This gene encodes a subunit of the intraflagellar transport complex A (IFT-A). IFT-A is a multiprotein complex that plays an important role in cilia assembly and maintenance by mediating retrograde ciliary transport. Mutations in this gene are a cause of cranioectodermal dysplasia-3 (CED3), also known as Sensenbrenner syndrome. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 112752 — RefSeq curated summary.

At a glance

• Gene–disease (curated): short-rib thoracic dysplasia 18 with polydactyly (Strong, GenCC) — +4 more curated relationships
• GWAS associations: 4
• Clinical variants (ClinVar): 341 total — 18 pathogenic, 23 likely-pathogenic
• Phenotypes (HPO): 106
• Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity unscored
• MANE Select transcript: NM_001102564

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29669
Approved symbol	IFT43
Name	intraflagellar transport 43
Location	14q24.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32173, MGC16028
Ensembl gene	ENSG00000119650
Ensembl biotype	protein_coding
OMIM	614068
Entrez	112752

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 10 protein_coding, 5 retained_intron, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000238628, ENST00000314067, ENST00000542766, ENST00000553338, ENST00000553438, ENST00000554026, ENST00000554233, ENST00000554423, ENST00000555305, ENST00000555370, ENST00000555677, ENST00000556742, ENST00000679083, ENST00000868357, ENST00000868358, ENST00000868359, ENST00000868360, ENST00000868361, ENST00000928220

RefSeq mRNA: 3 — MANE Select: NM_001102564 NM_001102564, NM_001255995, NM_052873

CCDS: CCDS41973, CCDS58330, CCDS9847

Canonical transcript exons

ENST00000314067 — 9 exons

Exon	Start	End
ENSE00000808439	76082617	76082692
ENSE00001252258	76083458	76083742
ENSE00001252292	76082295	76082367
ENSE00003526993	76059327	76059373
ENSE00003562064	76083227	76083289
ENSE00003652495	75988885	75988977
ENSE00003662232	76058642	76058674
ENSE00003691319	76022327	76022394
ENSE00003904670	75985763	75985840

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 97.19.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.9119 / max 100.8505, expressed in 1785 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
140709	17.9119	1785

Top tissues by expression

258 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	97.19	gold quality
bronchial epithelial cell	CL:0002328	96.51	gold quality
bronchus	UBERON:0002185	96.00	gold quality
kidney epithelium	UBERON:0004819	95.67	silver quality
cardiac muscle of right atrium	UBERON:0003379	95.61	silver quality
olfactory segment of nasal mucosa	UBERON:0005386	95.41	gold quality
adenohypophysis	UBERON:0002196	94.93	gold quality
right testis	UBERON:0004534	94.44	gold quality
pituitary gland	UBERON:0000007	94.39	gold quality
left testis	UBERON:0004533	94.39	gold quality
left ventricle myocardium	UBERON:0006566	93.86	silver quality
left lobe of thyroid gland	UBERON:0001120	93.68	gold quality
right lobe of thyroid gland	UBERON:0001119	93.58	gold quality
thyroid gland	UBERON:0002046	93.34	gold quality
testis	UBERON:0000473	93.30	gold quality
ascending aorta	UBERON:0001496	93.15	gold quality
ventricular zone	UBERON:0003053	93.13	gold quality
thoracic aorta	UBERON:0001515	93.03	gold quality
right atrium auricular region	UBERON:0006631	93.01	gold quality
cardiac atrium	UBERON:0002081	93.00	gold quality
islet of Langerhans	UBERON:0000006	92.89	gold quality
lower esophagus muscularis layer	UBERON:0035833	92.84	gold quality
lower esophagus	UBERON:0013473	92.83	gold quality
mucosa of paranasal sinus	UBERON:0005030	92.76	gold quality
adult mammalian kidney	UBERON:0000082	92.73	gold quality
body of uterus	UBERON:0009853	92.70	gold quality
endocervix	UBERON:0000458	92.67	gold quality
right lobe of liver	UBERON:0001114	92.62	gold quality
aorta	UBERON:0000947	92.52	gold quality
muscle layer of sigmoid colon	UBERON:0035805	92.51	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-114	yes	10.75
E-MTAB-6142	no	84.85
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

13 targeting IFT43, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-103A-1-5P	99.39	67.78	1545
HSA-MIR-103A-2-5P	99.39	67.72	1577
HSA-MIR-183-5P	99.31	72.27	1164
HSA-MIR-10399-5P	99.17	69.87	2610
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-3136-5P	98.53	67.68	793
HSA-MIR-4439	98.53	67.53	793
HSA-MIR-943	97.81	64.42	694
HSA-MIR-203A-5P	96.33	65.03	714
HSA-MIR-563	96.26	66.13	450
HSA-MIR-380-5P	95.68	67.32	512

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity Not yet evaluated (unscored). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 3)

• C14ORF179 encoding IFT43 is mutated in Sensenbrenner syndrome. (PMID:21378380)
• These results suggest that CED-4 forms a complex with ced-3 mRNA and delivers it to ribosomes for translation. (PMID:26740177)
• Studies identified a novel homozygous mutation in the ciliary protein IFT43 as the underlying cause of recessive inherited retinal degeneration. This is the first report demonstrating the involvement of IFT43 in retinal degeneration. (PMID:28973684)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ift43	ENSMUSG00000007867
rattus_norvegicus	Ift43	ENSRNOG00000010194

Protein

Protein identifiers

Intraflagellar transport protein 43 homolog — Q96FT9 (reviewed: Q96FT9)

All UniProt accessions (2): Q96FT9, A0A7I2V6B2

UniProt curated annotations — full annotation on UniProt →

Function. As a component of IFT complex A (IFT-A), a complex required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), it is involved in ciliogenesis. Involved in retrograde ciliary transport along microtubules from the ciliary tip to the base.

Subunit / interactions. Component of the IFT complex A (IFT-A) complex. IFT-A complex is divided into a core subcomplex composed of IFT122:IFT140:WDR19 which is associated with TULP3 and a peripheral subcomplex composed of IFT43:WDR35:TTC21B. Interacts directy with IFT122, WDR35 and TTC21B.

Subcellular location. Cytoplasm. Cytoskeleton. Cell projection. Cilium.

Tissue specificity. Expressed in the retina, predominantly in the photoreceptor outer segment.

Disease relevance. Cranioectodermal dysplasia 3 (CED3) [MIM:614099] A disorder primarily characterized by craniofacial, skeletal and ectodermal abnormalities. Clinical features include craniosynostosis, narrow rib cage, short limbs, brachydactyly, hypoplastic and widely spaced teeth, sparse hair, skin laxity and abnormal nails. Nephronophthisis leading to progressive renal failure, hepatic fibrosis, heart defects, and retinitis pigmentosa have also been described. The disease is caused by variants affecting the gene represented in this entry. Retinitis pigmentosa 81 (RP81) [MIM:617871] A form of retinitis pigmentosa, a retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. RP81 inheritance is autosomal recessive. The disease is caused by variants affecting the gene represented in this entry. Short-rib thoracic dysplasia 18 with polydactyly (SRTD18) [MIM:617866] A form of short-rib thoracic dysplasia, a group of autosomal recessive ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a ’trident’ appearance of the acetabular roof. Polydactyly is variably present. Non-skeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Some forms of the disease are lethal in the neonatal period due to respiratory insufficiency secondary to a severely restricted thoracic cage, whereas others are compatible with life. Disease spectrum encompasses Ellis-van Creveld syndrome, asphyxiating thoracic dystrophy (Jeune syndrome), Mainzer-Saldino syndrome, and short rib-polydactyly syndrome. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the IFT43 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q96FT9-1	1	yes
Q96FT9-2	2
Q96FT9-3	3
Q96FT9-4	4

RefSeq proteins (3): NP_001096034, NP_001242924, NP_443105 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029302	IFT43	Family

Pfam: PF15305

UniProt features (20 total): helix 5, sequence variant 4, splice variant 3, sequence conflict 2, modified residue 2, chain 1, region of interest 1, turn 1, compositionally biased region 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
8BBE	ELECTRON MICROSCOPY	3.5
8BBG	ELECTRON MICROSCOPY	3.5
8FGW	ELECTRON MICROSCOPY	3.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96FT9-F1	64.09	0.10

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 1, 78

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-5620924	Intraflagellar transport

MSigDB gene sets: 334 (showing top): STAT3_01, GOCC_MICROTUBULE_ORGANIZING_CENTER, chr14q24, GOBP_CILIUM_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, NKX22_01, RYTTCCTG_ETS2_B, GOBP_CELL_PROJECTION_ORGANIZATION, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, TGGAAA_NFAT_Q4_01, GOCC_CENTRIOLE, GOCC_CILIARY_TIP, GOCC_INTRACILIARY_TRANSPORT_PARTICLE, STAT1_01, GOCC_INTERCELLULAR_BRIDGE

GO Biological Process (3): intraciliary retrograde transport (GO:0035721), cilium assembly (GO:0060271), cell projection organization (GO:0030030)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (15): centriole (GO:0005814), cilium (GO:0005929), microtubule cytoskeleton (GO:0015630), intraciliary transport particle A (GO:0030991), perinuclear theca (GO:0033011), centriolar satellite (GO:0034451), ciliary basal body (GO:0036064), intercellular bridge (GO:0045171), mitotic spindle (GO:0072686), sperm principal piece (GO:0097228), sperm end piece (GO:0097229), ciliary tip (GO:0097542), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Assembly of the 9+0 primary cilium	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	7
microtubule organizing center	2
intracellular membraneless organelle	2
intraciliary transport particle	2
cytoskeleton	2
cilium	2
sperm flagellum	2
intraciliary transport	1
axoneme assembly	1
intraciliary transport involved in cilium assembly	1
cilium organization	1
protein localization to cilium	1
organelle assembly	1
trans-Golgi to periciliary membrane compartment transport	1
plasma membrane bounded cell projection assembly	1
ciliary transition zone assembly	1
cellular component organization	1
binding	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
protein-containing complex	1
perinuclear region of cytoplasm	1
centrosome	1
spindle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

544 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IFT43	WDR19	Q8NEZ3	997
IFT43	WDR35	Q9P2L0	997
IFT43	TTC21B	Q7Z4L5	996
IFT43	IFT140	Q96RY7	996
IFT43	IFT122	Q9HBG6	996
IFT43	IFT80	Q9P2H3	814
IFT43	IFT52	Q9Y366	790
IFT43	IFT46	Q9NQC8	775
IFT43	IFT20	Q8IY31	746
IFT43	DYNC2I2	Q96EX3	743
IFT43	IFT22	Q9H7X7	718
IFT43	IFT88	Q13099	706
IFT43	IFT172	Q9UG01	698
IFT43	DYNC2H1	Q8NCM8	694
IFT43	IFT57	Q9NWB7	692

IntAct

39 interactions, top by confidence:

A	B	Type	Score
WDR19	TULP3	psi-mi:“MI:0914”(association)	0.860
TULP3	TTC21B	psi-mi:“MI:0914”(association)	0.840
TTC21B	TULP3	psi-mi:“MI:0914”(association)	0.840
IFT122	IFT43	psi-mi:“MI:0915”(physical association)	0.800
TULP3	FOXK2	psi-mi:“MI:0914”(association)	0.790
IFT43	TULP3	psi-mi:“MI:0914”(association)	0.790
TTC21B	IFT43	psi-mi:“MI:0915”(physical association)	0.770
TTC21B	IFT43	psi-mi:“MI:0914”(association)	0.770
IFT43	WDR35	psi-mi:“MI:0915”(physical association)	0.740
WDR35	IFT43	psi-mi:“MI:0915”(physical association)	0.740
IFT122	TTC21B	psi-mi:“MI:0915”(physical association)	0.700
IFT43	ZMYND10	psi-mi:“MI:0915”(physical association)	0.560
IFT43	LMO2	psi-mi:“MI:0915”(physical association)	0.560
IFT43		psi-mi:“MI:0915”(physical association)	0.560
LMO2	IFT43	psi-mi:“MI:0915”(physical association)	0.560
TULP3	HSPG2	psi-mi:“MI:0914”(association)	0.530
IFT122	CDC7	psi-mi:“MI:0914”(association)	0.510
IFT140	ACSL3	psi-mi:“MI:0914”(association)	0.510
IFT122	IFT43	psi-mi:“MI:0915”(physical association)	0.400
IFT122	TTC21B	psi-mi:“MI:0915”(physical association)	0.400
WDR35	TTC21B	psi-mi:“MI:0914”(association)	0.350
IFT43	TLE1	psi-mi:“MI:0914”(association)	0.350

BioGRID (52): IFT43 (Two-hybrid), IFT43 (Two-hybrid), IFT43 (Affinity Capture-MS), IFT43 (Affinity Capture-MS), IFT122 (Affinity Capture-MS), TTC21B (Affinity Capture-MS), WDR35 (Affinity Capture-MS), C11orf74 (Affinity Capture-MS), WDR19 (Affinity Capture-MS), IFT140 (Affinity Capture-MS), TULP3 (Affinity Capture-MS), TYK2 (Affinity Capture-MS), SENP8 (Affinity Capture-MS), BBS1 (Affinity Capture-MS), TCEAL1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTI1, A2BIL8, A5PKK9, C5DY61, E2QSX5, E7F555, O35147, O43151, P11805, P19416, P24940, P27579, Q06616, Q17QE3, Q1LZE2, Q1RMQ5, Q1T763, Q28CW2, Q2HR82, Q2TBN9, Q3B8E9, Q3ZBS1, Q567C6, Q5RDK8, Q62417, Q68FW2, Q6AY26, Q6DFB0, Q6P6I6, Q6PKN7, Q80U49, Q86YL5, Q8C3W1, Q8QVM1, Q8VEB3, Q8VI59, Q96FT9, Q96GV9, Q96GY3, Q99618

Diamond homologs: A8HYP5, B5G1P1, B5X7E4, B5XBI1, E2QSX5, E7F555, Q28CW2, Q2TBN9, Q3B8E9, Q96FT9, Q9DA69

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
IFT43	“form complex”	“ITF complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 15 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Hedgehog ‘off’ state	6	82.4×	3e-09
Intraflagellar transport	5	77.1×	1e-07

GO biological processes:

GO term	Partners	Fold	FDR
intraciliary retrograde transport	5	374.5×	7e-11
protein localization to cilium	7	187.2×	4e-13
cilium assembly	5	24.5×	5e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

341 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	18
Likely pathogenic	23
Uncertain significance	112
Likely benign	133
Benign	22

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1074375	NM_001102564.3(IFT43):c.174_175delinsAT (p.Cys58_Arg59delinsTer)	Pathogenic
1404794	NM_001102564.3(IFT43):c.296-5646dup	Pathogenic
1451154	NM_001102564.3(IFT43):c.342del (p.Phe114fs)	Pathogenic
1452113	NM_001102564.3(IFT43):c.1A>C (p.Met1Leu)	Pathogenic
1452896	NM_001102564.3(IFT43):c.296-5612_296-5611insCTCAC	Pathogenic
155306	GRCh38/hg38 14q11.2-32.33(chr14:20043514-106877229)x3	Pathogenic
1923321	NM_001102564.3(IFT43):c.341_342del (p.Phe114fs)	Pathogenic
2135504	NM_001102564.3(IFT43):c.136_137del (p.Leu46fs)	Pathogenic
2427153	NC_000014.8:g.(?76420747)(76455340_?)del	Pathogenic
2829572	NM_001102564.3(IFT43):c.296-5613del	Pathogenic
31098	NM_001102564.3(IFT43):c.1A>G (p.Met1Val)	Pathogenic
3611348	NM_001102564.3(IFT43):c.296-5638_296-5637del	Pathogenic
3611403	NM_001102564.3(IFT43):c.296-5656C>A	Pathogenic
4277718	NM_001102564.3(IFT43):c.296-5634_296-5633del	Pathogenic
4694554	NM_001102564.3(IFT43):c.94C>T (p.Gln32Ter)	Pathogenic
4714720	NM_001102564.3(IFT43):c.296-5618C>G	Pathogenic
488649	NM_001102564.3(IFT43):c.2T>A (p.Met1Lys)	Pathogenic
968952	NM_001102564.3(IFT43):c.25G>T (p.Glu9Ter)	Pathogenic
1338759	NM_001102564.3(IFT43):c.509ATG[1] (p.Asp171del)	Likely pathogenic
1495638	NM_001102564.3(IFT43):c.368+2T>A	Likely pathogenic
1513672	NM_001102564.3(IFT43):c.148-2A>C	Likely pathogenic
2070174	NM_001102564.3(IFT43):c.54+2T>A	Likely pathogenic
2079123	NM_001102564.3(IFT43):c.296-1G>T	Likely pathogenic
2427155	NC_000014.8:g.(?76542999)(76544540_?)del	Likely pathogenic
2695673	NM_001102564.3(IFT43):c.296-1G>C	Likely pathogenic
2999696	NM_001102564.3(IFT43):c.296-5699G>T	Likely pathogenic
3576768	NM_001102564.3(IFT43):c.20T>A (p.Leu7Ter)	Likely pathogenic
3576770	NM_001102564.3(IFT43):c.55del (p.Arg19fs)	Likely pathogenic
3576774	NM_001102564.3(IFT43):c.164T>A (p.Leu55Ter)	Likely pathogenic
3576775	NM_001102564.3(IFT43):c.175C>T (p.Arg59Ter)	Likely pathogenic

SpliceAI

3642 predictions. Top by Δscore:

Variant	Effect	Δscore
14:75961012:T:TA	donor_gain	1.0000
14:75963350:T:TA	donor_gain	1.0000
14:75963485:CGC:C	acceptor_gain	1.0000
14:75963486:GCC:G	acceptor_loss	1.0000
14:75963488:C:CC	acceptor_gain	1.0000
14:75964493:A:AC	donor_gain	1.0000
14:75964494:C:CC	donor_gain	1.0000
14:75964510:A:C	donor_gain	1.0000
14:75965696:C:CC	acceptor_gain	1.0000
14:75971125:CCT:C	donor_gain	1.0000
14:75971251:AGGAT:A	acceptor_gain	1.0000
14:75971256:C:CC	acceptor_gain	1.0000
14:75971256:C:T	acceptor_loss	1.0000
14:75971257:T:C	acceptor_loss	1.0000
14:75971550:GTTAC:G	donor_loss	1.0000
14:75971551:TTA:T	donor_loss	1.0000
14:75971552:TA:T	donor_loss	1.0000
14:75971714:TTCGT:T	acceptor_gain	1.0000
14:75971715:TCGT:T	acceptor_gain	1.0000
14:75971716:CGT:C	acceptor_gain	1.0000
14:75971716:CGTC:C	acceptor_gain	1.0000
14:75971717:GTC:G	acceptor_loss	1.0000
14:75971718:TCT:T	acceptor_loss	1.0000
14:75971719:C:CC	acceptor_gain	1.0000
14:75971719:C:CG	acceptor_loss	1.0000
14:75971720:T:G	acceptor_loss	1.0000
14:75971726:A:C	acceptor_gain	1.0000
14:75980540:A:AC	donor_gain	1.0000
14:75980541:C:CC	donor_gain	1.0000
14:75980541:CT:C	donor_gain	1.0000

AlphaMissense

1355 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:76083470:T:A	W174R	0.998
14:76083470:T:C	W174R	0.998
14:76083472:G:C	W174C	0.996
14:76083472:G:T	W174C	0.996
14:76083252:T:A	L157H	0.995
14:76082652:T:C	L135P	0.994
14:76083243:T:C	L154P	0.993
14:76083264:T:C	L161P	0.993
14:76083264:T:A	L161H	0.991
14:76083471:G:C	W174S	0.991
14:76083252:T:G	L157R	0.990
14:76083486:T:C	L179P	0.990
14:76083252:T:C	L157P	0.988
14:76083478:G:C	W176C	0.986
14:76083478:G:T	W176C	0.986
14:76082307:T:C	I103T	0.985
14:76083476:T:A	W176R	0.983
14:76083476:T:C	W176R	0.983
14:76082652:T:A	L135Q	0.981
14:76082664:T:C	L139P	0.981
14:76083500:T:C	S184P	0.981
14:76082355:C:A	A119E	0.979
14:76083264:T:G	L161R	0.979
14:75988900:C:A	R24S	0.976
14:76082642:T:G	Y132D	0.976
14:76083243:T:A	L154Q	0.976
14:76083471:G:T	W174L	0.976
14:76083470:T:G	W174G	0.975
14:76083282:T:A	V167D	0.974
14:76083503:T:C	S185P	0.974

dbSNP variants (sampled 300 via entrez): RS1000021600 (14:76082547 G>A), RS1000037024 (14:75995611 C>T), RS1000040807 (14:76080033 T>G), RS1000071717 (14:76068556 AATGACCTC>A), RS1000097528 (14:76039573 C>G), RS1000117803 (14:76079623 C>T), RS1000170859 (14:76079313 C>T), RS1000269335 (14:76036230 G>A,C), RS1000271260 (14:76051407 A>G,T), RS1000317821 (14:76043418 T>C), RS1000322840 (14:76045913 G>A), RS1000338126 (14:76015354 C>T), RS1000343567 (14:76029980 A>G), RS1000388878 (14:75988378 A>G), RS1000433519 (14:76076851 G>T)

Disease associations

OMIM: gene MIM:614068 | disease phenotypes: MIM:614099, MIM:617871, MIM:617866, MIM:208500

GenCC curated gene-disease

Disease	Classification	Inheritance
retinitis pigmentosa 81	Strong	Autosomal recessive
short-rib thoracic dysplasia 18 with polydactyly	Strong	Autosomal recessive
cranioectodermal dysplasia 3	Strong	Autosomal recessive
cranioectodermal dysplasia	Supportive	Autosomal recessive
ciliopathy	Limited	Autosomal recessive

Mondo (9): cranioectodermal dysplasia 3 (MONDO:0013573), retinitis pigmentosa 81 (MONDO:0036482), short-rib thoracic dysplasia 18 with polydactyly (MONDO:0036483), connective tissue disorder (MONDO:0003900), prostate cancer (MONDO:0008315), Jeune syndrome (MONDO:0018770), short rib-polydactyly syndrome (MONDO:0015461), ciliopathy (MONDO:0005308), cranioectodermal dysplasia (MONDO:0009032)

Orphanet (4): Cranioectodermal dysplasia (Orphanet:1515), Familial prostate cancer (Orphanet:1331), Jeune syndrome (Orphanet:474), Short rib-polydactyly syndrome (Orphanet:1505)

HPO phenotypes

106 total (30 of 106 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000090	Nephronophthisis
HP:0000113	Polycystic kidney dysplasia
HP:0000164	Abnormality of the dentition
HP:0000219	Thin upper lip vermilion
HP:0000232	Everted lower lip vermilion
HP:0000238	Hydrocephalus
HP:0000256	Macrocephaly
HP:0000268	Dolichocephaly
HP:0000269	Prominent occiput
HP:0000286	Epicanthus
HP:0000316	Hypertelorism
HP:0000347	Micrognathia
HP:0000405	Conductive hearing impairment
HP:0000407	Sensorineural hearing impairment
HP:0000463	Anteverted nares
HP:0000476	Cystic hygroma
HP:0000501	Glaucoma
HP:0000505	Visual impairment
HP:0000506	Telecanthus
HP:0000512	Abnormal electroretinogram
HP:0000543	Optic disc pallor
HP:0000545	Myopia
HP:0000546	Retinal degeneration
HP:0000551	Color vision defect
HP:0000563	Keratoconus
HP:0000601	Hypotelorism
HP:0000602	Ophthalmoplegia
HP:0000613	Photophobia
HP:0000618	Blindness

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST002263_2	Acute urticaria and angioedema (non-steroidal anti-inflammatory drug-induced)	1.000000e-06
GCST002263_5	Acute urticaria and angioedema (non-steroidal anti-inflammatory drug-induced)	1.000000e-06
GCST007581_13	Carpal tunnel syndrome	1.000000e-08
GCST007880_5	Emotional lability in attention deficit hyperactivity disorder	4.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005533	response to non-steroidal anti-inflammatory
EFO:0008475	mood instability measurement

MeSH disease descriptors (4)

Descriptor	Name	Tree numbers
D003240	Connective Tissue Diseases	C17.300
D011471	Prostatic Neoplasms	C04.588.945.440.770; C12.100.500.260.750; C12.100.500.565.625; C12.200.294.260.750; C12.200.294.565.625; C12.200.758.409.750; C12.900.619.750
D012779	Short Rib-Polydactyly Syndrome	C05.116.099.708.857; C05.660.585.600.750; C16.131.077.850; C16.131.621.585.600.750
C537571	Jeune syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	2
arsenite	affects binding, increases reaction	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
abrine	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	decreases expression	1
Cadmium	increases abundance, increases expression	1
Coumestrol	decreases expression, affects cotreatment	1
Demecolcine	increases expression	1
Dexamethasone	decreases expression	1
Doxorubicin	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Phthalic Acids	increases methylation	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tunicamycin	increases expression	1
Vincristine	increases expression	1
Cyclosporine	increases expression	1
Cadmium Chloride	increases abundance, increases expression	1

Clinical trials (associated diseases)

305 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT01042158	PHASE4	COMPLETED	A Clinical Trial of Ambrisentan and Tadalafil in Pulmonary Arterial Hypertension Associated With Systemic Sclerosis
NCT03688191	PHASE4	UNKNOWN	Study of Sirolimus in CTD-TP in China
NCT04169100	PHASE4	UNKNOWN	Novel Form of Acquired Long QT Syndrome
NCT04197050	PHASE4	UNKNOWN	Effect of Sacubitril/Valsartan on Reduced Right Ventricular Ejection Fraction in Patients With CTD
NCT04928586	PHASE4	UNKNOWN	Immunosuppressant Combined With Pirfenidone in CTD-ILD
NCT05440240	PHASE4	RECRUITING	Percutaneous Needle Fasciotomy +/- Corticosteroid Injection for Dupuytren’s Contracture
NCT05505409	PHASE4	UNKNOWN	Efficacy and Safety of Pirfenidone in CTD-ILD
NCT06499233	PHASE4	RECRUITING	Efficacy and Safety of Prophylactic Treatment for Pneumocystis Jirovecii Pneumonia in Patients With Autoimmune Inflammatory Rheumatic Disease
NCT00029224	PHASE4	COMPLETED	Treatment With Zoledronic Acid in Patients With Breast Cancer, Multiple Myeloma, and Prostate Cancer With Cancer Related Bone Lesions
NCT00035997	PHASE4	COMPLETED	Open-label Trial on the Effect of I.V. Zoledronic Acid 4 mg on Bone Density in Hormone Sensitive Prostate Cancer Patients With Bone Metastasis
NCT00063609	PHASE4	COMPLETED	The Effect of Zoledronic Acid on Bone Loss in Prostate Cancer Patients Undergoing Androgen Deprivation Therapy
NCT00103623	PHASE4	SUSPENDED	The Plenaxis® Experience Study
NCT00106392	PHASE4	COMPLETED	A Safety and Efficacy Study of Prograf in the Prevention of Erectile Dysfunction After Radical Prostatectomy
NCT00185029	PHASE4	UNKNOWN	MR-Lymphography and Lymph Node Staging in Prostate Cancer
NCT00199485	PHASE4	COMPLETED	Angelica Sinensis for the Treatment of Hot Flashes in Men Undergoing LHRH Therapy for Prostate Cancer
NCT00219219	PHASE4	COMPLETED	Zoledronic Acid in the Prevention of Skeletal-related Events in Hormone Refractory and Hormone-sensitive Prostate Cancer Patients With Bone Metastases
NCT00219271	PHASE4	COMPLETED	Effect Of Zoledronic Acid On Circulating And Bone Marrow-Residing Prostate Cancer Cells In Patients With Clinically Localized Prostate Cancer
NCT00237146	PHASE4	COMPLETED	Study to Evaluate Zoledronic Acid on Quality of Life and Skeletal-related Events as Adjuvant Treatment in Patients With Hormone-naïve Prostate Cancer and Bone Metastasis Who Have Undergone Orchiectomy
NCT00242554	PHASE4	COMPLETED	Open-label Phase IV Clinical Trial to Evaluate the Safety and Tolerability of Zoledronic Acid in Patients With Prostate Cancer and Bone Metastases
NCT00280098	PHASE4	COMPLETED	Docetaxel in the Treatment of Hormone Refractory Prostate Cancer
NCT00293696	PHASE4	COMPLETED	Casodex/Zoladex Biomarkers in Localised Prostate Cancer
NCT00334139	PHASE4	COMPLETED	Effect of Zoledronic Acid on Bone Metabolism in Patients With Bone Metastasis and Prostate or Breast Cancer
NCT00375765	PHASE4	COMPLETED	Effects On Dihydrotestosterone Regulated Gene Expression In Benign Prostatic Hyperplasia Or Prostate Cancer
NCT00391690	PHASE4	COMPLETED	Evaluation of Bone Markers as Diagnostic Tools for Early Detection of Bone Metastases in Patients With High Risk Prostate Cancer
NCT00422708	PHASE4	COMPLETED	Local Anesthesia for Prostate Biopsy
NCT00526331	PHASE4	COMPLETED	Evaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00590213	PHASE4	COMPLETED	Compare the Value of Prophylactic Versus Therapeutic Breast Radiotherapy in CASODEX
NCT00629330	PHASE4	TERMINATED	Dissemination of Prostate Cancer Screening to PCP’s in African American Communities
NCT00771966	PHASE4	COMPLETED	Radical Prostatectomy and Perioperative Fluid Therapy
NCT00805701	PHASE4	COMPLETED	Study Assessing The Efficacy And Safety Of Avodart (Dutasteride) At Improving Urinary Symptoms In Men With Prostate Cancer Who Are Undergoing Seed Implantation
NCT00859027	PHASE4	COMPLETED	Effect Of Risedronate On Bone Mass In Older Men Receiving Neoadjuvant Therapy For Prostate Cancer
NCT00906269	PHASE4	UNKNOWN	Can Hyperbaric Oxygen Improve Erectile Function Following Surgery for Prostate Cancer
NCT00953277	PHASE4	COMPLETED	Study of Nerve Reconstruction Using AVANCE in Subjects Who Undergo Robotic Assisted Prostatectomy for Treatment of Prostate Cancer
NCT00982800	PHASE4	COMPLETED	Does Postoperative Gabapentin Reduce Pain, Opioid Consumption and Anxiety and Have a Positive Effect on Health Related Quality of Life After Radical Prostatectomy?
NCT01083199	PHASE4	COMPLETED	Global Performance Evaluation of the AMS CONTINUUM™ Device
NCT01136226	PHASE4	COMPLETED	Evaluate Recovery of Testosterone for Patients Using Eligard
NCT01161563	PHASE4	COMPLETED	Randomized Crossover Trial to Assess the Tolerability of Gonadotropin Releasing Hormone (GnRH) Analogue Administration
NCT01230905	PHASE4	COMPLETED	Study to Monitor the Effects of Androgen Suppression Treatment on the Heart
NCT01296672	PHASE4	COMPLETED	3 Month Finasteride Challenge Test Can Significantly Improve the Performance of Screening for Prostate Cancer
NCT01365143	PHASE4	TERMINATED	Prospective Randomized Trial Comparing Robotic Versus Open Radical Prostatectomy